Table 3.

Distribution of substitutions and indels within different sequence regions amongst haplotypes

Sequence region	Base pairs	COX		QBL		SSTO		APD		DBB		MANN		MCF
		S	ID	S	ID	S	ID	S	ID	S	ID	S	ID	S	ID
Coding	247,505	353	8	503	19	380	2	74	0	351	6	401	9	348	2
UTR	155,960	382	34	438	59	331	35	38	9	326	39	303	35	309	31
Intronic	1,283,472	3,141	571	3,135	590	2,658	505	602	147	2,897	509	2,185	393	2,126	404
Total intragenic	1,686,937	3,876	613	4,076	668	3,369	542	714	156	3,574	554	2,889	437	2,783	437
Pseudogenic	57,223	235	15	226	21	227	19	101	8	191	10	109	6	113	10
Pseudogenic intron	63,108	507	54	220	27	215	18	158	20	258	22	98	13	179	13
Transcript exon	78,092	190	30	207	33	119	22	71	8	136	17	88	16	70	15
Transcript intron	332,705	1,243	197	1,186	216	1,053	155	85	29	1,245	192	1,081	161	268	53
REPEATS:
LINEs	608,429	2,110	221	2,015	240	2,388	255	755	93	2,097	217	2,084	193	1,530	164
SINEs	428,567	1,381	428	1,316	401	1,311	385	346	134	1,229	318	928	241	936	271
Other repeats	487,863	2,605	207	2,518	229	2,514	207	925	56	2,748	199	2,198	177	2,170	169
Total in repeats	1,524,859	6,096	856	5,849	870	6,213	847	2,026	283	6,074	734	5,210	611	4,636	604
Microsatellite	15,185	186	168	95	85	222	198	14	29	60	76	61	71	90	68
All above	3,297,590	12,333	1,933	11,859	1,920	11,418	1,801	3,169	533	11,538	1,605	9,536	1,315	8,139	1,200
Other intergenic	996,720	3,634	460	3,423	440	3,564	499	1,061	150	2,717	370	2,566	339	2,651	345
Total	4,754,829	15,967	2,393	15,282	2,360	14,982	2,300	4,230	683	14,255	1,975	12,102	1,654	10,790	1,545

Variations shown in Table 2 ascribed to sequence regions identified during annotation. These included exonic, UTR and intronic regions of coding; pseudogenic and transcript loci; repeat elements, microsatellites and other intergenic regions

S Substitution, ID indel